The Adaptive Immune Response Flashcards

Adaptive Immune Response: Generation of Diversity, B Cells, and Antibodies

Learning Objectives

• Describe the creation of a diverse repertoire of lymphocytes, detailing the genetic mechanisms and cellular processes involved.

• Name and describe the different effector functions of antibodies, including their roles in neutralization, opsonization, and complement activation.

• Understand the difference between T-dependent and T-independent B cell responses, outlining the molecular interactions and cellular requirements for each.

• Describe B cell activation, proliferation, and maturation, including the role of T cell help and the germinal center, with a focus on the signaling pathways and transcriptional regulators involved.

• Know the difference between isotype class-switching, somatic hypermutation, and affinity maturation, detailing the enzymatic activities and cellular locations where these processes occur.

Basic Principles of the Adaptive Immune System

• Start with a very diverse repertoire to increase the chance of finding a match to a pathogen. This diversity is generated through V(D)J recombination and junctional diversity.

• Expand (and improve, in some cases) the matched cell. Clonal expansion and somatic hypermutation enhance the immune response.

• Maintain some of these matched cells for future "memory" against the pathogen. Memory B and T cells provide long-term immunity.

Defining B Cell and T Cell Pathogen Recognition

• T Cell Receptor:

  • \gamma\delta or \alpha\beta

  • Membrane-bound

  • Recognizes peptide antigen presented by MHC on other cells. The TCR interacts with the MHC-peptide complex, triggering T cell activation.

• B Cell Receptor:

  • Heavy and light chain

  • Membrane-bound OR soluble as antibody

  • Recognizes antigens on whole molecules. BCRs can bind to a wide range of antigens, including proteins, polysaccharides, and lipids.

  • Can be different isotypes depending on the Fc region. The isotype determines the effector function of the antibody.

B Cells and Antibodies

• B cells start with the receptor on the cell surface (BCR), which recognizes whole antigens. This recognition triggers B cell activation and differentiation.

• They differentiate into plasma cells that secrete the receptor as antibody. Plasma cells are highly specialized for antibody production.

• Antibodies bind to whole pathogens and facilitate a range of functions depending on their Fc region. The Fc region interacts with effector cells and molecules.

Importance of Antibodies

• Neutralization: Blocks toxins and viruses from interacting with cells. Antibodies prevent pathogen entry into host cells.

• Opsonization: Promotes phagocytosis and killing activity by other cells. Antibodies enhance the uptake of pathogens by phagocytes.

• Complement Activation: Helps kill pathogens. The classical complement pathway is initiated by antibody binding to pathogens.

• Agglutination: Agglutinates particles (pathogen debris, viruses etc.). Agglutination increases the efficiency of pathogen clearance.

• ADCC: Mediates Antibody-dependent cell-mediated cytotoxicity. NK cells and other cytotoxic cells are activated by antibody-coated target cells.

Overview of B Cell Development

• B cell development occurs in the bone marrow. This is where B cells undergo V(D)J recombination and negative selection.

• It involves stages such as stem cell, early pro-B cell, late pro-B cell, large pre-B cell, small pre-B cell, immature B cell, and mature B cell. Each stage is characterized by specific gene rearrangements and protein expression patterns.

• Antigen exposure leads to antigen-specific clonal expansion. Only B cells that recognize the antigen are expanded.

• Germinal center reactions include hypermutation in the dark zone and selection in the light zone. These reactions refine the antibody response.

• This process leads to the formation of plasma cells and memory B cells. Plasma cells secrete antibodies, while memory B cells provide long-term immunity.

B Cell Development and Diversity

• B cells were originally discovered in the Bursa Fabricus in chickens. This organ is responsible for B cell development in birds.

• Initial generation of diversity (gene rearrangement and heterodimer formation) happens before exposure to exogenous antigen. This ensures a diverse repertoire of B cells capable of recognizing a wide range of pathogens.

• In B cells, this occurs in the bone marrow; in T cells, it happens in the thymus. The bone marrow and thymus are the primary lymphoid organs for B and T cell development, respectively.

BCR/Antibody Structure

• Variable region with two binding sites determines antigen specificity (Fv region). The variable region is formed by the V(D)J segments.

• The constant region (Fc region) determines the class of the antibody and its function. The constant region interacts with effector molecules and cells.

• Antibodies consist of two identical heavy chains and two identical light chains. These chains are linked by disulfide bonds.

Lymphocyte Generation of Diversity

• B Cell Receptor (Bone Marrow):

  • Gene Rearrangement: Heavy and Light chain (x2). V(D)J recombination generates diversity in the heavy and light chains.

• T Cell Receptor (Thymus):

  • Heterodimer formation (\alpha with \beta or \gamma with \delta). TCR diversity is generated through heterodimer formation and V(D)J recombination.

• VDJ gene rearrangement occurs in heavy, beta, and delta genes. This process combines different V, D, and J gene segments to form a unique variable region.

• VJ gene rearrangement occurs in light (kappa or lambda), alpha, and gamma genes. This process combines V and J gene segments to form a unique variable region.

• Hypermutation and Class Switching occur only in B cells. These processes refine the antibody response in the germinal center.

Diversity of B Cell Receptors/Antibodies

• The human genome has 3 billion base pairs, but only 20,000-25,000 genes. This limited number of genes is insufficient to encode the vast diversity of antibodies needed to recognize all possible pathogens.

• Microbial diversity is estimated to be around half a million different species. The immune system must be able to recognize and respond to this vast array of pathogens.

Gene Rearrangement as a Solution to Pathogen Diversity

• Gene rearrangement combines different gene segments to create one whole gene. This allows a limited number of gene segments to generate a vast diversity of antibodies.

• RAG1 and RAG2 (Recombination Activating Genes) are the enzymes that facilitate this process. These enzymes recognize and cleave DNA at specific recombination signal sequences (RSS).

• Variable (V), Diversity (D), and Joining (J) regions are involved. These regions are combined in different ways to generate unique variable regions.

Variable Region Gene Segments

• Variable regions of the antibody are made up of two or three gene segments – VJ (light chain) or VDJ (heavy chain). The arrangement of these segments determines the antigen-binding specificity of the antibody.

• Light chains can be either kappa or lambda. These are two different types of light chains that can be combined with a heavy chain to form an antibody.

Immunoglobulin Gene Rearrangement

• IGHV, IGHD, and IGHJ regions are involved in heavy chain rearrangement. These regions are located on the heavy chain locus and are combined to form the heavy chain variable region.

• Framework regions (Fw1, Fw2, Fw3) and Complementarity Determining Regions (CDR1, CDR2, CDR3) are important. Framework regions provide structural support, while CDRs are responsible for antigen binding.

Mathematics of Combinatorial Diversity

• If there are 4 genes in group 1, 3 in group 2, and 2 in group 3, then the number of possible protein combinations is calculated as: 4 \times 3 \times 2 = 24

Scaling Up Combinatorial Diversity

• If there are 6 genes in group 1, 4 in group 2, and 3 in group 3, then the number of possible protein combinations is calculated as: 6 \times 4 \times 3 = 72

Ig Gene Rearrangement Mathematics

• Immunoglobulin Heavy Chain:

  • 61 IGHV regions

  • 26 IGHD regions

  • 6 IGHJ regions

  • Total combinations: 61 \times 26 \times 6 = 9516

• Immunoglobulin Light Chain:

  • (40 IGLV regions x 7 IGL) + (48 IGKV regions x 5 IGKJ) = 520

• The number of possible combinations: 9516 \times 520 = 4.9 \times 10^6

Junctional Region Diversity

• Additional diversity is created at the junction where different gene segments join together. This is due to the imprecise joining of gene segments.

• Nucleotides can be accidentally removed or deliberately inserted (by Terminal deoxynucleotidyl Transferase - TdT). This process adds or removes nucleotides at the junctions, further increasing diversity.

Antibody Diversity, Class Switching, and Hypermutation

• Estimates suggest that we can make around 10 billion different antibodies. This vast diversity is essential for recognizing and responding to the wide range of pathogens encountered throughout life.

• Class switching allows an antibody to change its function. This process changes the constant region of the heavy chain, altering the effector function of the antibody while maintaining antigen specificity.

• Hypermutation of the variable region can improve the affinity of the antibody. This process introduces mutations into the variable region, allowing for the selection of B cells with higher affinity for the antigen.

Post-Activation B Cell Development

• B Cell Receptor (Bone Marrow): Gene Rearrangement, Heavy and Light chain (x2)

• T Cell Receptor (Thymus): Heterodimer formation (\alpha with \beta or \gamma with \delta)

• B cells undergo Hypermutation and Class Switching, which are unique to B cells. These processes occur in the germinal center and require T cell help.

Hypermutation and Class Switching

• Happen AFTER B cell activation. These processes are initiated by antigen binding to the BCR and subsequent T cell help.

• Require help from T helper (Th2) cells, cytokines, and contact with other cells. Th2 cells provide cytokines and co-stimulatory signals that are essential for hypermutation and class switching.

• Take place in the germinal center and require the enzyme Activation Induced Cytidine Deaminase (AID). AID is responsible for initiating somatic hypermutation and class switching by deaminating cytosine residues in DNA.

Class Switching

• Keeps the antigen specificity in the variable region. The variable region remains unchanged during class switching, ensuring that the antibody retains its original antigen specificity.

• Switches the class (and therefore function) of the antibody. Class switching changes the constant region of the heavy chain, altering the effector function of the antibody.

Arrangement of Constant Region Genes at the IgH Locus

• Genes: Cμ, Cδ, Cγ3, Cγ1, Cα1, Cγ2, Cγ4, Cε, Cα2

• Isotypes: IgM, IgD, IgG3, IgG1, IgA1, IgG2, IgG4, IgE, IgA2

Classes and Subclasses of Antibody

• IgM, IgD, IgG, IgA, IgE are the major classes of antibodies. Each class has a distinct structure and function.

• IgG has subclasses (IgG1, IgG2, IgG3, IgG4). These subclasses have different effector functions and tissue distributions.

• IgA has subtypes (IgA1, IgA2). These subtypes are found in different mucosal tissues.

Antibody Classes

• IgD:

  • Membrane-bound form on Naive B cells. Its function is to signal when the B cell is ready to be activated.

• IgM:

  • The default immunoglobulin B cells start with.

  • Forms pentamers. This structure allows IgM to bind to multiple antigens simultaneously.

  • Efficient at activating complement. IgM is the most effective antibody at initiating the classical complement pathway.

• IgG:

  • Main antibody secreted into the blood after class switching. IgG is the most abundant antibody in serum.

  • Good at opsonization. IgG enhances the uptake of pathogens by phagocytes.

  • Mediates antibody-dependent cellular cytotoxicity by NK cells. IgG activates NK cells to kill target cells.

  • Has 4 subclasses. Each subclass has a different affinity for Fc receptors and complement proteins.

• IgA:

  • The mucosal antibody. IgA is the predominant antibody in mucosal secretions.

  • Secreted into breast milk. IgA provides passive immunity to newborns.

  • Can form a dimer. This structure allows IgA to bind to multiple antigens in mucosal tissues.

  • Has two Subtypes. These subtypes have different distributions in mucosal tissues.

• IgE:

  • Important in parasitic infection. IgE mediates the immune response to parasites.

  • Binds to mast cells. IgE activates mast cells to release inflammatory mediators.

  • Involved in allergy and immediate hypersensitivity. IgE is responsible for allergic reactions.

Class Switching

• Can be direct from IgM or indirect via another isotype. The order of class switching is determined by the arrangement of constant region genes on the IgH locus.

Somatic Hypermutation

• Deliberate mutation of Ig genes. This process introduces mutations into the variable region of the antibody.

• Multi-step process starting with the enzyme AID at hotspots. AID initiates somatic hypermutation by deaminating cytosine residues in DNA.

• Occurs in the germinal center. The germinal center provides the environment necessary for somatic hypermutation and affinity maturation.

B Cell Development - Germinal Center

• occurs in bone marrow.

• antigen specific clonal Expansion happens.

• Hypermutation occurs in the dark zone.

• selection in the Light Zone.

Germinal Center B Cell Responses

• Involves T cell zone, mantle cell zone, and marginal zone. Each zone plays a distinct role in B cell development and activation.

B Cell Expansion and Mutation

• B cells that recognize the pathogen expand. This clonal expansion increases the number of B cells specific for the pathogen.

• As B cells expand, they mutate their Ig genes and the best ones are kept. This process of mutation and selection leads to affinity maturation.

Germinal Center Affinity Maturation

• Involves multiple cycles of mutation and selection. This process refines the antibody response, resulting in antibodies with higher affinity for the antigen.

• Follicular helper T cells (TFH) and Follicular Dendritic Cells (FDC) are key players. TFH cells provide help to B cells, while FDCs present antigen to B cells.

• Occurs in the dark and light zones. The dark zone is where somatic hypermutation occurs, while the light zone is where selection occurs.

B Cell Activation

• Three types of antigens can activate B cells: T-independent type I (TI-I), T-independent type II (TI-II), and T-dependent (TD). Each type of antigen activates B cells through a different mechanism.

• Various receptors are involved, including the B cell receptor, innate immune receptors, co-stimulatory molecules, and cytokines. These receptors and molecules play a role in B cell activation and differentiation.

• Co-stimulation and cytokines are produced by helper cells, like CD4+ Tfh cells. These signals are essential for B cell activation and differentiation.

T-Independent Type I (TI-1) Antigens

• Polyclonal activators that don't need a specific receptor. TI-1 antigens activate B cells regardless of their antigen specificity.

• e.g., via TLRs (Pattern recognition receptors). TI-1 antigens can activate B cells by binding to TLRs.

T-Independent Type II (TI-2) Antigens

• Large molecules with a repeating determinant. TI-2 antigens have repetitive structures that can cross-link BCRs.

• Bind to multiple receptors on the cell surface, causing cross-linking and activation. This cross-linking triggers B cell activation.

• Traditionally said that no memory B cells are formed. However, recent studies suggest that some memory B cells may be formed in response to TI-2 antigens.

T-Dependent (TD) Antigens

• Protein antigens. TD antigens require T cell help to activate B cells.

• B cells process and present the peptide antigen on the surface with MHC class II molecules to recruit T cell help. This allows T cells to recognize and interact with B cells.

• Memory B cells are formed. TD antigens induce the formation of long-lived memory B cells.

B-T Interactions

• The BCR captures antigen to present to the T cell ("Signal 1"). This is the first signal required for B cell activation.

• Signalling between T cell CD4 and B cell MHC II.

• Antigen internalization and processing.

• Up-regulation of Co-stimulatory molecules.

T Cell Help for B Cells

• The T cell provides helpful signals to the B cell (e.g., CD40-CD40L (CD154) interaction - "Signal 2"). This is the second signal required for B cell activation.

• TNF-R family of molecules involved in B cell proliferation, differentiation, isotype switching, upregulation of surface molecules, and germinal center development. These molecules play a crucial role in B cell responses.

Overview of T-Dependent B Cell Response

• Involves naive B cells, B cell blasts, germinal center B cells, mutated memory B cells, mutated long-lived plasma cells.

• Naive T cells, unmutated short-lived plasma cells (IgM) are also involved.

• Occurs in extrafollicular regions and germinal center follicles.

Maturation of the Response

• Maturation of the response takes time, which is why vaccination is so important. Vaccination allows the immune system to develop a mature and effective response to a pathogen before exposure.